But didn't he say that if gays can have sex and not get arrested then incest (among others) should be 'legal' too?No, that's not what he said.
What he was talking about is the legal foundation for such laws. He said nothing about what should or should not be legal.
If the Supreme Court finds that there exists a right to privacy in the home that means that sodomy laws must be thrown out, then the same ruling would mean the end of all those other laws, since they have the same legal foundation.
Obviously, he thinks that would be a very bad thing, which is why he is making the argument that striking down the legal foundation for the sodomy laws would be a very bad thing.
You might want to read this article if you haven't, because the author actually examines the very point Santorum is making, and concedes that Santorum's point is not easily answered.